Settlements and champions need to become increasingly divergent and specialized as they level up. In addition to choosing buildings and traits, each level should bring bonuses and or penalties that further this specialization.
Fortresses need more level-by-level increase to what they are designed to do, for example.
Champions such as a mage should gain spell school or summoning increases in addition to the random perks. Assassins could get more crit damage and chance, while a defender gets more ZOC and unit protection powers. A warrior should get better at killing stuff--possibly including the + to number of figures in a unit he can attack (if you go that route.)
While some increases may be happening already, they need to be more drastic, and explained on level up.